Watkins is very very good, but has been hurt. He was not hurt in college, so how could he know and who knows if he will not be injured after his foot heals? In hindsight, there were other great WRs in that draft (OBJ and Mike Evans), so maybe trading the extra 1st was questionable.
The point about EJ is off-base. EJ was supposed to sit and learn as a rookie, Kevin Kolb got hurt and couldn't play. EJ actually wasn't horrid as a rookie, even when they knew whe was not ready to play. In year 2, Orton was not clearly better than Manuel, but Marrone wanted to play the vet. I don't think that Orton played well enough to keep Manuel on the bench, but that is water under the bridge.
Overall, I am comfortable with Whaley's drafting - I think finding a QB IS hard unless the team totally crashes.